Mystery manga containing supernatural beings
Manga
Mystery manga that contain supernatural/mythological/folklore beings. May only make mention of these things or may actually be set in a world where they're real. "Beings" includes creatures, spirits, youkai, gods e.t.c. People with supernatural powers are not included.
Only series focusing on or centred around said beings have been added. Only the first entry has been added if it's part of a series.
Only series focusing on or centred around said beings have been added. Only the first entry has been added if it's part of a series.

Manga, ? vol, 2020
Me:-
Author:7
Contains youkai. Adapted from a novel (no MAL entry).
Kurosagi Shitai Takuhaibin
The Kurosagi Corpse Delivery Service

Manga, ? vol, 2000
Me:-
Author:8
Contains ghosts/spirits.
Mayonaka no Occult Koumuin
Midnight occult civil servants

Manga, 17 vol, 2015
Me:-
Author:7
Has a bit of everything (e.g. angels and tengu).

Manga, 4 vol, 2013
Me:-
Author:8
Contains mouryou. Part of a series, each adapted from novels (only the first book has a MAL entry).

Manga, ? vol, 2016
Me:-
Author:4
Contains supernatural beings such as vampires and demons. Adapted from a novel (no MAL entry).

Manga, 12 vol, 1997
Me:-
Author:8
As the name suggests, contains ghosts. Has a sequel. Adapted from light novels.
Hanako to Guuwa no Teller
Hanako and the Terror of Allegory

Manga, 4 vol, 2003
Me:-
Author:6
Contains folklore beings/urban legends.

Manga, 7 vol, 1999
Me:-
Author:4
Contains many Norse Gods/Goddesses in human form. Part of a series.

Manga, 2 vol, 2007
Me:-
Author:6
As the name suggests, contains mononoke. Part of a series, each one direct adaptations of every arc in the anime.
Umineko no Naku Koro ni - Episode 1: Legend of the Golden Witch
Umineko When They Cry Episode 1: Legend of the Golden Witch

Manga, 4 vol, 2007
Me:-
Author:7
Contains witches and other supernatural beings. Part of a series.

Manga, 10 vol, 1999
Me:-
Author:7
Contains things called mushi; it kind of fits the bill of supernatural creatures so I've included it. Has a sequel.

Manga, 10 vol, 2009
Me:-
Author:5
As the name suggests, contains demons. Loses some of the "mystery" aspect of it as the manga progresses though.

Manga, 14 vol, 2009
Me:-
Author:8
Contains ghosts and spirits. Adapted from a novel.
Yumekui Kenbun
Nightmare Inspector: Yumekui Kenbun

Manga, 9 vol, 2001
Me:-
Author:8
Contains a baku (supernatural being).

Manga, 19 vol, 2003
Me:-
Author:10
Contains spirits/youkai/supernatural beings. Has a sequel. You'll want to read Tsubasa Reservoir Chronicle at the same time to make sense of the plot.

Manga, 10 vol, 1995
Me:-
Author:6
Contains many "exotic" creatures. Has a sequel.

Light Novel, 6 vol, 2006
Me:-
Author:-
Contains supernatural beings such as vampires. Part of a series. Light novels, also available in manga form.
Bakemono Yawazukushi
Phantom Tales of the Night

Manga, 12 vol, 2016
Me:-
Author:-
Contains ghosts/spirits.

Manga, 3 vol, 1999
Me:-
Author:9
Contains supernatural beings, gods and seirei. Spin-off of Discommunication but you can read this without having read it (though it does provide some context). Both Discommunication and Yume Tsukai (the sequel/alternate universe) could possibly be on this list but I think this one fit best.
Kyokou Suiri
In/Spectre

Manga, ? vol, 2015
Me:-
Author:-
Contains spirits and supernatural beings/urban legends. Adapted from a novel.

Manga, 5 vol, 2010
Me:-
Author:5
Contains supernatural and demonic creatures. Adapted from light novels.

Light Novel, ? vol, 2007
Me:-
Author:-
Contains "demons". Part of the Type-Moon universe (though you can read it without prior Nasuverse/Type-Moon knowledge).
"Bungaku Shoujo" Series
Book Girl

Light Novel, 8 vol, 2006
Me:-
Author:-
Contains a youkai. Light novels, also available in manga form.
Halloween Tantei Oz Williams
Halloween Detective Oz Williams

Manga, 3 vol, 2012
Me:-
Author:6
Contains spirits/supernatural beings and death gods.
Touhou Suzunaan: Forbidden Scrollery.
Forbidden Scrollery

Manga, 7 vol, 2012
Me:-
Author:-
Contains youkai. Part of the Touhou universe (though you can read it without prior knowledge).
Karasuma Kyouko no Jikenbo
Kyoko Karasuma the detective of Asakusa police department.

Manga, 10 vol, 2002
Me:-
Author:5
Contains youkai.
Muhyo to Rouji no Mahouritsu Soudan Jimusho
Muhyo & Roji's Bureau of Supernatural Investigation

Manga, 18 vol, 2004
Me:-
Author:7
Contains ghosts. Loses the "mystery" aspect quite quickly though.